Myrna stops in Align stage

[kyungeun]

hi i'm trying to align on myrna some human RNA sequence, paired, illumina with Ensemble 58 ref..


Myrna stops in Align stage..
My args is

-D mapred.reduce.tasks=0 -input s3n://gmi-ewha/AK1/data/web_prepro -output hdfs:///myrna/intermediate/6448/align -mapper 's3n://myrna-emr/1.0.9/Align.pl --discard-reads=0 --ref=S3N://myrna-refs/human_ensembl_58.jar --destdir=/mnt/6448 --partlen=1000000 --qual=phred33 --truncate=0 --globals=HDFS:///myrna/intermediate/6448/globals --discard-mate=0 --pool-trim-length=0 -- --partition -1000000 --mm -t --hadoopout --startverbose -l 10 -m 1 -n 3 -X 550 -I450 -q' -cacheFile s3n://myrna-emr/1.0.9/bowtie64#bowtie -cacheFile s3n://myrna-emr/1.0.9/Get.pm#Get.pm -cacheFile s3n://myrna-emr/1.0.9/Util.pm#Util.pm -cacheFile s3n://myrna-emr/1.0.9/Tools.pm#Tools.pm -cacheFile s3n://myrna-emr/1.0.9/AWS.pm#AWS.pm

this is my error message

log4j:WARN No appenders could be found for logger (org.apache.hadoop.conf.Configuration).
log4j:WARN Please initialize the log4j system properly.
Align.pl: s3cmd: found: /usr/bin/s3cmd, given:
Align.pl: jar: found: /usr/lib/jvm/java-6-sun/bin/jar, given:
Align.pl: hadoop: found: /home/hadoop/bin/../bin/hadoop, given:
Align.pl: wget: found: /usr/bin/wget, given:
Align.pl: s3cfg:
Align.pl: bowtie: found: ./bowtie, given:
Align.pl: partition len: 1000000
Align.pl: ref: S3N://myrna-refs/human_ensembl_58.jar
Align.pl: quality: solexa64
Align.pl: truncate at: 0
Align.pl: discard mate: 0
Align.pl: discard reads < truncate len: 0
Align.pl: SAM passthrough: 0
Align.pl: Straight through: 0
Align.pl: globals directory: HDFS:///myrna/intermediate/26527/globals
Align.pl: pool replicates?: 0
Align.pl: pool trim length: 0
Align.pl: pool technical replicates?: 0
Align.pl: local index path:
Align.pl: bowtie args: --partition -1000000 --mm -t --hadoopout --startverbose -l 10 -m 1 -n 3 -X 550 -I 450 -q
Align.pl: ls -al
Align.pl: total 52
drwxr-xr-x 3 hadoop hadoop 4096 2010-09-19 08:22 .
drwxr-xr-x 3 hadoop hadoop 4096 2010-09-19 08:22 ..
lrwxrwxrwx 1 hadoop hadoop 81 2010-09-19 08:22 Align.pl -> /mnt1/var/lib/hadoop/mapred/taskTracker/archive/myrna-emr/1.0.9/Align.pl/Align.pl
lrwxrwxrwx 1 hadoop hadoop 77 2010-09-19 08:22 AWS.pm -> /mnt2/var/lib/hadoop/mapred/taskTracker/archive/myrna-emr/1.0.9/AWS.pm/AWS.pm
lrwxrwxrwx 1 hadoop hadoop 80 2010-09-19 08:22 bowtie -> /mnt/var/lib/hadoop/mapred/taskTracker/archive/myrna-emr/1.0.9/bowtie64/bowtie64
lrwxrwxrwx 1 hadoop hadoop 77 2010-09-19 08:22 Get.pm -> /mnt3/var/lib/hadoop/mapred/taskTracker/archive/myrna-emr/1.0.9/Get.pm/Get.pm
lrwxrwxrwx 1 hadoop hadoop 82 2010-09-19 08:22 job.jar -> /mnt/var/lib/hadoop/mapred/taskTracker/jobcache/job_201009190807_0002/jars/job.jar
lrwxrwxrwx 1 hadoop hadoop 87 2010-09-19 08:22 .job.jar.crc -> /mnt/var/lib/hadoop/mapred/taskTracker/jobcache/job_201009190807_0002/jars/.job.jar.crc
lrwxrwxrwx 1 hadoop hadoop 83 2010-09-19 08:22 META-INF -> /mnt/var/lib/hadoop/mapred/taskTracker/jobcache/job_201009190807_0002/jars/META-INF
lrwxrwxrwx 1 hadoop hadoop 78 2010-09-19 08:22 org -> /mnt/var/lib/hadoop/mapred/taskTracker/jobcache/job_201009190807_0002/jars/org
drwxr-xr-x 2 hadoop hadoop 4096 2010-09-19 08:22 tmp
lrwxrwxrwx 1 hadoop hadoop 81 2010-09-19 08:22 Tools.pm -> /mnt1/var/lib/hadoop/mapred/taskTracker/archive/myrna-emr/1.0.9/Tools.pm/Tools.pm
lrwxrwxrwx 1 hadoop hadoop 78 2010-09-19 08:22 Util.pm -> /mnt/var/lib/hadoop/mapred/taskTracker/archive/myrna-emr/1.0.9/Util.pm/Util.pm
Align.pl: Read first line of stdin:
FN:s_2_1_sequence_8M.txt;LB:Tumor-Subject1-lane1;RN:@GA05_0001:1:12:3560:11869#0/2 CTTAAAAATACTCTCCTCAAGTTAATTTAAATGCAATGCCAATAACAATTGTAATGTTTTGTTTACCATTTTATGTAACCTACATGATAATGACATAGCCT
Bad number of read tokens ; expected 3 or 5:
FN:s_2_1_sequence_8M.txt;LB:Tumor-Subject1-lane1;RN:@GA05_0001:1:12:3560:11869#0/2 CTTAAAAATACTCTCCTCAAGTTAATTTAAATGCAATGCCAATAACAATTGTAATGTTTTGTTTACCATTTTATGTAACCTACATGATAATGACATAGCCT

i don't know what is meaning of these error and these sentence(Bad number of read tokens ; expected 3 or 5: ).

please reply me..

thank you.